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  <div class="section" id="calc-dislocation-monopole-py">
<h1>calc_dislocation_monopole.py<a class="headerlink" href="#calc-dislocation-monopole-py" title="Permalink to this headline">¶</a></h1>
<div class="section" id="module-iprPy.calculation.dislocation_monopole.calc_dislocation_monopole">
<span id="calculation-script-functions"></span><h2>Calculation script functions<a class="headerlink" href="#module-iprPy.calculation.dislocation_monopole.calc_dislocation_monopole" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="iprPy.calculation.dislocation_monopole.calc_dislocation_monopole.anneal_info">
<code class="sig-name descname">anneal_info</code><span class="sig-paren">(</span><em class="sig-param">temperature=0.0</em>, <em class="sig-param">runsteps=None</em>, <em class="sig-param">randomseed=None</em>, <em class="sig-param">units='metal'</em><span class="sig-paren">)</span><a class="headerlink" href="#iprPy.calculation.dislocation_monopole.calc_dislocation_monopole.anneal_info" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates LAMMPS commands for thermo anneal.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>temperature</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a><em>, </em><em>optional</em>) – The temperature to relax at (default is 0.0).</p></li>
<li><p><strong>randomseed</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.8)"><em>int</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.8)"><em>None</em></a><em>, </em><em>optional</em>) – Random number seed used by LAMMPS in creating velocities and with
the Langevin thermostat.  (Default is None which will select a
random int between 1 and 900000000.)</p></li>
<li><p><strong>units</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)"><em>str</em></a><em>, </em><em>optional</em>) – The LAMMPS units style to use (default is ‘metal’).</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The generated LAMMPS input lines for performing a dynamic relax.
Will be ‘’ if temperature==0.0.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)">str</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="iprPy.calculation.dislocation_monopole.calc_dislocation_monopole.disl_relax">
<code class="sig-name descname">disl_relax</code><span class="sig-paren">(</span><em class="sig-param">lammps_command</em>, <em class="sig-param">system</em>, <em class="sig-param">potential</em>, <em class="sig-param">mpi_command=None</em>, <em class="sig-param">annealtemp=0.0</em>, <em class="sig-param">annealsteps=None</em>, <em class="sig-param">randomseed=None</em>, <em class="sig-param">etol=0.0</em>, <em class="sig-param">ftol=1e-06</em>, <em class="sig-param">maxiter=10000</em>, <em class="sig-param">maxeval=100000</em>, <em class="sig-param">dmax=0.01</em><span class="sig-paren">)</span><a class="headerlink" href="#iprPy.calculation.dislocation_monopole.calc_dislocation_monopole.disl_relax" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets up and runs the disl_relax.in LAMMPS script for relaxing a
dislocation monopole system.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>lammps_command</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)"><em>str</em></a>) – Command for running LAMMPS.</p></li>
<li><p><strong>system</strong> (<em>atomman.System</em>) – The system to perform the calculation on.</p></li>
<li><p><strong>potential</strong> (<em>atomman.lammps.Potential</em>) – The LAMMPS implemented potential to use.</p></li>
<li><p><strong>mpi_command</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)"><em>str</em></a><em>, </em><em>optional</em>) – The MPI command for running LAMMPS in parallel.  If not given, LAMMPS
will run serially.</p></li>
<li><p><strong>annealtemp</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a><em>, </em><em>optional</em>) – The temperature to perform a dynamic relaxation at. Default is 0.0,
which will skip the dynamic relaxation.</p></li>
<li><p><strong>annealsteps</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.8)"><em>int</em></a><em>, </em><em>optional</em>) – The number of time steps to run the dynamic relaxation for.  Default
is None, which will run for 10000 steps if annealtemp is not 0.0.</p></li>
<li><p><strong>randomseed</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.8)"><em>int</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.8)"><em>None</em></a><em>, </em><em>optional</em>) – Random number seed used by LAMMPS in creating velocities and with
the Langevin thermostat.  Default is None which will select a
random int between 1 and 900000000.</p></li>
<li><p><strong>etol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a><em>, </em><em>optional</em>) – The energy tolerance for the structure minimization. This value is
unitless. Default is 0.0.</p></li>
<li><p><strong>ftol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a><em>, </em><em>optional</em>) – The force tolerance for the structure minimization. This value is in
units of force. Default is 0.0.</p></li>
<li><p><strong>maxiter</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.8)"><em>int</em></a><em>, </em><em>optional</em>) – The maximum number of minimization iterations to use default is
10000.</p></li>
<li><p><strong>maxeval</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.8)"><em>int</em></a><em>, </em><em>optional</em>) – The maximum number of minimization evaluations to use default is
100000.</p></li>
<li><p><strong>dmax</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a><em>, </em><em>optional</em>) – The maximum distance in length units that any atom is allowed to relax
in any direction during a single minimization iteration default is
0.01 Angstroms.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><p>Dictionary of results consisting of keys:</p>
<ul class="simple">
<li><p><strong>’logfile’</strong> (<em>str</em>) - The name of the LAMMPS log file.</p></li>
<li><p><strong>’dumpfile’</strong> (<em>str</em>) - The name of the LAMMPS dump file
for the relaxed system.</p></li>
<li><p><strong>’E_total’</strong> (<em>float</em>) - The total potential energy for the
relaxed system.</p></li>
</ul>
</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.8)">dict</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="iprPy.calculation.dislocation_monopole.calc_dislocation_monopole.dislocationmonopole">
<code class="sig-name descname">dislocationmonopole</code><span class="sig-paren">(</span><em class="sig-param">lammps_command, ucell, potential, C, burgers, ξ_uvw, slip_hkl, mpi_command=None, m=[0, 1, 0], n=[0, 0, 1], sizemults=None, amin=None, bmin=None, cmin=None, shift=None, shiftscale=False, shiftindex=None, tol=1e-08, etol=0.0, ftol=0.0, maxiter=10000, maxeval=100000, dmax=0.01, annealtemp=0.0, annealsteps=None, randomseed=None, boundaryshape='cylinder', boundarywidth=0.0, boundaryscale=False</em><span class="sig-paren">)</span><a class="headerlink" href="#iprPy.calculation.dislocation_monopole.calc_dislocation_monopole.dislocationmonopole" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates and relaxes a dislocation monopole system.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>lammps_command</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)"><em>str</em></a>) – Command for running LAMMPS.</p></li>
<li><p><strong>ucell</strong> (<em>atomman.System</em>) – The unit cell to use as the seed for generating the dislocation
monopole system.</p></li>
<li><p><strong>potential</strong> (<em>atomman.lammps.Potential</em>) – The LAMMPS implemented potential to use.</p></li>
<li><p><strong>C</strong> (<em>atomman.ElasticConstants</em>) – The elastic constants associated with the bulk crystal structure
for ucell.</p></li>
<li><p><strong>burgers</strong> (<em>array-like object</em>) – The dislocation’s Burgers vector given as a Miller or
Miller-Bravais vector relative to ucell.</p></li>
<li><p><strong>ξ_uvw</strong> (<em>array-like object</em>) – The dislocation’s line direction given as a Miller or
Miller-Bravais vector relative to ucell.</p></li>
<li><p><strong>slip_hkl</strong> (<em>array-like object</em>) – The dislocation’s slip plane given as a Miller or Miller-Bravais
plane relative to ucell.</p></li>
<li><p><strong>mpi_command</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.8)"><em>None</em></a><em>, </em><em>optional</em>) – The MPI command for running LAMMPS in parallel.  If not given, LAMMPS
will run serially.</p></li>
<li><p><strong>m</strong> (<em>array-like object</em><em>, </em><em>optional</em>) – The m unit vector for the dislocation solution.  m, n, and ξ
(dislocation line) should be right-hand orthogonal.  Default value
is [0,1,0] (y-axis).</p></li>
<li><p><strong>n</strong> (<em>array-like object</em><em>, </em><em>optional</em>) – The n unit vector for the dislocation solution.  m, n, and ξ
(dislocation line) should be right-hand orthogonal.  Default value
is [0,0,1] (z-axis). n is normal to the dislocation slip plane.</p></li>
<li><p><strong>sizemults</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.8)"><em>tuple</em></a><em>, </em><em>optional</em>) – The size multipliers to use when generating the system.  Values are
limited to being positive integers.  The multipliers for the two
non-periodic directions must be even.  If not given, the default
multipliers will be 2 for the non-periodic directions and 1 for the
periodic direction.</p></li>
<li><p><strong>amin</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a><em>, </em><em>optional</em>) – A minimum thickness to use for the a box vector direction of the
final system.  Default value is 0.0.  For the non-periodic
directions, the resulting vector multiplier will be even.  If both
amin and sizemults is given, then the larger multiplier for the two
will be used.</p></li>
<li><p><strong>bmin</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a><em>, </em><em>optional</em>) – A minimum thickness to use for the b box vector direction of the
final system.  Default value is 0.0.  For the non-periodic
directions, the resulting vector multiplier will be even.  If both
bmin and sizemults is given, then the larger multiplier for the two
will be used.</p></li>
<li><p><strong>cmin</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a><em>, </em><em>optional</em>) – A minimum thickness to use for the c box vector direction of the
final system.  Default value is 0.0.  For the non-periodic
directions, the resulting vector multiplier will be even.  If both
cmin and sizemults is given, then the larger multiplier for the two
will be used.</p></li>
<li><p><strong>shift</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a><em>, </em><em>optional</em>) – A rigid body shift to apply to the rotated cell prior to inserting
the dislocation.  Should be selected such that the ideal slip plane
does not correspond to any atomic planes.  Is taken as absolute if
shiftscale is False, or relative to the rotated cell’s box vectors
if shiftscale is True.  Cannot be given with shiftindex.  If
neither shift nor shiftindex is given then shiftindex = 0 is used.</p></li>
<li><p><strong>shiftindex</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a><em>, </em><em>optional</em>) – The index of the identified optimum shifts based on the rotated
cell to use.  Different values allow for the selection of different
atomic planes neighboring the slip plane.  Note that shiftindex
values only apply shifts normal to the slip plane; best shifts for
non-planar dislocations (like bcc screw) may also need a shift in
the slip plane.  Cannot be given with shiftindex.  If neither shift
nor shiftindex is given then shiftindex = 0 is used.</p></li>
<li><p><strong>shiftscale</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.8)"><em>bool</em></a><em>, </em><em>optional</em>) – If False (default), a given shift value will be taken as absolute
Cartesian.  If True, a given shift will be taken relative to the
rotated cell’s box vectors.</p></li>
<li><p><strong>tol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a>) – A cutoff tolerance used with obtaining the dislocation solution.
Only needs to be changed if there are issues with obtaining a
solution.</p></li>
<li><p><strong>etol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a><em>, </em><em>optional</em>) – The energy tolerance for the structure minimization. This value is
unitless. Default is 0.0.</p></li>
<li><p><strong>ftol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a><em>, </em><em>optional</em>) – The force tolerance for the structure minimization. This value is in
units of force. Default is 0.0.</p></li>
<li><p><strong>maxiter</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.8)"><em>int</em></a><em>, </em><em>optional</em>) – The maximum number of minimization iterations to use. Default is
10000.</p></li>
<li><p><strong>maxeval</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.8)"><em>int</em></a><em>, </em><em>optional</em>) – The maximum number of minimization evaluations to use. Default is
100000.</p></li>
<li><p><strong>dmax</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a><em>, </em><em>optional</em>) – The maximum distance in length units that any atom is allowed to relax
in any direction during a single minimization iteration. Default is
0.01 Angstroms.</p></li>
<li><p><strong>annealtemp</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a><em>, </em><em>optional</em>) – The temperature to perform a dynamic relaxation at. Default is 0.0,
which will skip the dynamic relaxation.</p></li>
<li><p><strong>annealsteps</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.8)"><em>int</em></a><em>, </em><em>optional</em>) – The number of time steps to run the dynamic relaxation for.  Default
is None, which will run for 10000 steps if annealtemp is not 0.0.</p></li>
<li><p><strong>randomseed</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.8)"><em>int</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.8)"><em>None</em></a><em>, </em><em>optional</em>) – Random number seed used by LAMMPS in creating velocities and with
the Langevin thermostat.  Default is None which will select a
random int between 1 and 900000000.</p></li>
<li><p><strong>boundaryshape</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)"><em>str</em></a><em>, </em><em>optional</em>) – Indicates the shape of the boundary region to use.  Options are
‘cylinder’ (default) and ‘box’.  For ‘cylinder’, the non-boundary
region is defined by a cylinder with axis along the dislocation
line and a radius that ensures the boundary is at least
boundarywidth thick.  For ‘box’, the boundary region will be
exactly boundarywidth thick all around.</p></li>
<li><p><strong>boundarywidth</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.8)"><em>float</em></a><em>, </em><em>optional</em>) – The width of the boundary region to apply.  Default value is 0.0,
i.e. no boundary region.  All atoms in the boundary region will
have their atype values changed.</p></li>
<li><p><strong>boundaryscale</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.8)"><em>bool</em></a><em>, </em><em>optional</em>) – If False (Default), the boundarywidth will be taken as absolute.
If True, the boundarywidth will be taken relative to the magnitude
of the unit cell’s a box vector.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><p>Dictionary of results consisting of keys:</p>
<ul class="simple">
<li><p><strong>’dumpfile_base’</strong> (<em>str</em>) - The filename of the LAMMPS dump file
for the relaxed base system.</p></li>
<li><p><strong>’symbols_base’</strong> (<em>list of str</em>) - The list of element-model
symbols for the Potential that correspond to the base system’s
atypes.</p></li>
<li><p><strong>’dumpfile_disl’</strong> (<em>str</em>) - The filename of the LAMMPS dump file
for the relaxed dislocation monopole system.</p></li>
<li><p><strong>’symbols_disl’</strong> (<em>list of str</em>) - The list of element-model
symbols for the Potential that correspond to the dislocation
monopole system’s atypes.</p></li>
<li><p><strong>’dislocation’</strong> (<em>atomman.defect.Dislocation</em>) - The Dislocation
object used to generate the monopole system.</p></li>
<li><p><strong>’E_total_disl’</strong> (<em>float</em>) - The total potential energy of the
dislocation monopole system.</p></li>
</ul>
</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.8)">dict</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="iprPy.calculation.dislocation_monopole.calc_dislocation_monopole.main">
<code class="sig-name descname">main</code><span class="sig-paren">(</span><em class="sig-param">*args</em><span class="sig-paren">)</span><a class="headerlink" href="#iprPy.calculation.dislocation_monopole.calc_dislocation_monopole.main" title="Permalink to this definition">¶</a></dt>
<dd><p>Main function called when script is executed directly.</p>
</dd></dl>

<dl class="function">
<dt id="iprPy.calculation.dislocation_monopole.calc_dislocation_monopole.process_input">
<code class="sig-name descname">process_input</code><span class="sig-paren">(</span><em class="sig-param">input_dict</em>, <em class="sig-param">UUID=None</em>, <em class="sig-param">build=True</em><span class="sig-paren">)</span><a class="headerlink" href="#iprPy.calculation.dislocation_monopole.calc_dislocation_monopole.process_input" title="Permalink to this definition">¶</a></dt>
<dd><p>Processes str input parameters, assigns default values if needed, and
generates new, more complex terms as used by the calculation.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>input_dict</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.8)"><em>dict</em></a>) – Dictionary containing the calculation input parameters with string
values.  The allowed keys depends on the calculation style.</p></li>
<li><p><strong>UUID</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.8)"><em>str</em></a><em>, </em><em>optional</em>) – Unique identifier to use for the calculation instance.  If not
given and a ‘UUID’ key is not in input_dict, then a random UUID4
hash tag will be assigned.</p></li>
<li><p><strong>build</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.8)"><em>bool</em></a><em>, </em><em>optional</em>) – Indicates if all complex terms are to be built.  A value of False
allows for default values to be assigned even if some inputs
required by the calculation are incomplete.  (Default is True.)</p></li>
</ul>
</dd>
</dl>
</dd></dl>

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